Hi Emmanuel-
Thanks for fixing the whitespace issue. I think this fix will be useful to many
users.
On the issue of recognizing 10 IUPAC characters: I think this is a real
problem, and may come up again in short order. Maybe it is just that use of
this function has been limited? In the single dataset with a modest number of
sequences that caused me problems yesterday, I had the following species and/or
genus names - all of which constitute 10 character strings drawn from the set
of IUPAC codes:
brachyurus (x 2)
savannarum
graduacauda
caudacutus
Camarhynchus (x 3)
madagascariensis
I don't suggest deprecating the phylip sequential, but rather, using something
that is compatible with raxml (surely one of the most widely used phylogenetics
programs today). I think raxml uses a relaxed sequential version of the phylip
format with whitespace delimitation. I could read the same alignment in raxml
with no problems, but I had multiple issues when reading the same file with
read.dna (including the whitespace character on the first line). My guess is
that very few people are using the original phylip format, with its limit of 10
characters per taxon name, and with dna seqs beginning immediately after this.
So maybe deprecate "sequential phylip", but you could use what Stamatakis calls
"relaxed sequential PHYLIP", which appears to be: (1) taxon names cannot
include spaces but can be up to 100 characters; and (2) names separated from
sequences by whitespace character (ideally, this should recognize any number of
spaces or tabs to prevent user confusion).
For users with tab-delimited raxml files (eg each taxon name separated from its
dna sequence by a tab), you can use a regular-expressions enabled text editor
(like textwrangler) to quickly find potential problems. Just search for
[ACGTUMRWSYKVHDBN]{10}.+\t
with grep matching enabled.
Cheers,
~Dan
On Apr 26, 2012, at 2:16 AM, Emmanuel Paradis wrote:
> Hi Dan,
>
> The reason for this implementation (searching the first 10 IUPAC-coded bases)
> is because the exact formatting is not inconsistent among different programs.
> Some files have:
>
> 0123456789acgt.....
>
> that is a 10-character name and the sequence starting on the 11th position. I
> think this is typical for Phylip. Other software (e.g., PhyML) accepts longer
> taxa names and require a space before the start of the sequence.
>
> About your example: it depends on the order of the data. The following file
> can be read:
>
> 2 10
> xxxxx AAAAAAAAAA
> madagascarAAAAAAAAAA
>
> But if you invert the two sequence lines, it fails.
>
> It is the first time I hear about this problem in 9 years, maybe because it
> requires a particular combination of circumstances. Another drawback of this
> implementation is that files with less than 10 bases cannot be read.
>
> How to solve this? If it were left only to me, I would deprecate the
> interleaved and sequential formats. FASTA is more flexible, more widespread,
> easier to parse, can store exactly the same information, and labels are only
> constrained to be on a single line (but can contain any characters including
> \n, \t, ...) But I guess many programs use the Phylip formats, so I'd be glad
> to read other suggestions.
>
> As for your 2nd problem, it is now fixed in ape.
>
> Best,
>
> Emmanuel
> -----Original Message-----
> From: Dan Rabosky <[email protected]>
> Sender: [email protected]
> Date: Wed, 25 Apr 2012 17:51:35
> To: <[email protected]>
> Subject: [R-sig-phylo] read.dna warnings and pitfalls
>
>
> Hi All-
>
> I have spent an inordinate and embarrassing amount of time tracking down an
> excruciatingly cryptic issue with read.dna, which I rarely use. Here are two
> key problems:
>
> 1) The function automatically assumes it is reading DNA sequences when it
> encounters a string of 10 continuous "DNA-like" characters. This includes all
> characters in the set (ACGTUMRWSYKVHDBN-). This function, unlike the phylip
> original, does not have limits on taxon name lengths. Hence, I had - in the
> middle of a large alignment - a species whose name included the string
> "MADAGASCAR", which caused a failure. To be fair, the documentation warns of
> this, but I think this is extremely easy to overlook, and - moreover - it
> seems unfortunate to have to parse all your taxon names for a potential IUPAC
> match before trying to use the function. Presumably, most users who specify
> sequential spacing will be using whitespace to separate taxon names from DNA
> sequences, and perhaps it is better to exploit this rather than IUPAC
> matching.
>
> 2) The function is whitespace-sensitive. if you tab-separate the numbers on
> the first line (numbers of taxa, numbers of sites), you'll receive an errror
> with the message: "the first line of the file must contain the dimensions of
> the data". It appears that spaces are OK, however.
>
> Hopefully this post will be useful to somewhere in the future with a similar
> issue. Perhaps these can be addressed in a future update to ape?
>
> -Dan Rabosky
>
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